GROMACS version:2022
GROMACS modification:No
Hello all,
I am having trouble converting my modified residue to rtp format.
I methylated my residue
ATOM 781 N ARG A 130 8.714 54.987 2.676 1.00 47.63 N
ATOM 782 CA ARG A 130 9.061 56.391 2.868 1.00 47.63 C
ATOM 783 C ARG A 130 9.052 57.092 1.516 1.00 47.63 C
ATOM 784 O ARG A 130 8.614 58.234 1.401 1.00 47.63 O
ATOM 785 CB ARG A 130 10.437 56.528 3.519 1.00 76.92 C
ATOM 786 CG ARG A 130 10.508 55.943 4.915 1.00 76.92 C
ATOM 787 CD ARG A 130 11.825 56.267 5.593 1.00 76.92 C
ATOM 788 NE ARG A 130 11.900 55.657 6.916 1.00 76.92 N
ATOM 789 CZ ARG A 130 12.901 55.838 7.770 1.00 76.92 C
ATOM 790 NH1 ARG A 130 13.923 56.618 7.443 1.00 76.92 N1+
ATOM 791 NH2 ARG A 130 12.882 55.239 8.953 1.00 76.92 N
ATOM 792 C01 ARG A 130 13.991 55.440 9.897 0.00 0.00 C
ATOM 793 C02 ARG A 130 11.752 54.374 9.321 0.00 0.00 C
ATOM 794 H02 ARG A 130 14.312 54.511 10.265 0.00 0.00 H
ATOM 795 H05 ARG A 130 11.340 54.701 10.229 0.00 0.00 H
ATOM 796 H03 ARG A 130 13.667 56.040 10.695 0.00 0.00 H
ATOM 797 H06 ARG A 130 12.088 53.384 9.424 0.00 0.00 H
ATOM 798 H04 ARG A 130 14.787 55.915 9.404 0.00 0.00 H
ATOM 799 H07 ARG A 130 11.020 54.417 8.569 0.00 0.00 H
then used cgenff to generate a itp to convert to an rtp
; Atom type charge
O2 OG2D1 -0.548 1 ;carbonyl O
N NH1 -0.4700 2 ;peptide nitrogen
N2 NG2D1 -0.824 3 ;N for neutral imine/Schiff's base C=N-R
N3 NG301 -0.137 4 ;neutral trimethylamine nitrogen
N4 NG321 -0.502 5 ;neutral methylamine
C1 CG321 -0.281 6 ;C for CH2
C3 CG321 -0.196 7 ;C for CH2
C4 CG311 0.326 8 ;ch
C5 CG321 0.015 9 ;C for CH2
C2 CG2O2 0.779 10 ;carbonyl C peptide backbone
C6 CG2N1 0.500 11 ;conjugated C in guanidine
C7 CG331 -0.207 12 ;C for methyl group CH3
C8 CG331 -0.207 13 ;C for methyl group CH3
H1 HGA2 0.090 14 ;alphatic proton, CH2
H2 HGA2 0.090 15 ;alphatic proton, CH2
H3 HGA2 0.090 16 ;alphatic proton, CH2
H4 HGA2 0.090 17 ;alphatic proton, CH2
H5 HGA1 0.090 18 ;alphatic proton, CH
H6 HGA2 0.090 19 ;alphatic proton, CH2
H7 HGA2 0.090 20 ;alphatic proton, CH2
H10 HGA3 0.090 23 ;alphatic proton, CH3
H11 HGA3 0.090 24 ;alphatic proton, CH3
H12 HGA3 0.090 25 ;alphatic proton, CH3
H13 HGA3 0.090 26 ;alphatic proton, CH3
H14 HGA3 0.090 27 ;alphatic proton, CH3
H15 HGA3 0.090 28 ;alphatic proton, CH3
Because I have to add hydrogens for cgenff and the atom names dont carry over I have lost track of my hydrogens. Can someone help me with the error when I use pdb2gmx
Fatal error:
Atom N in residue AMA 130 was not found in rtp entry AMA with 32 atoms
while sorting atoms.
.
is there a way to label files when switiching formats from pdb to mol2 to str to itp
since I have tried to label my mol2 and rtp could someone tell me why there is an error in applying my rtp to my pdb?
rtp
; Name
[ AMA ]
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
N1 NG321 -1.081 ;neutral methylamine
C1 CG311 0.369 ;ch
C2 CG2O4 0.142 ;carbonyl C aldehyde
O1 OG2D1 -0.389 ;carbonyl O
C3 CG321 -0.196 ;C for CH2
C4 CG321 -0.196 ;C for CH2
C5 CG321 0.015 ;C for CH2
N2 NG2D1 -0.824 ;N for neutral imine/Schiff's base C=N-R
C6 CG2N1 0.500 ;conjugated C in guanidine
N3 NG321 -0.502 ;neutral methylamine
N4 NG301 -0.137 ;neutral trimethylamine nitrogen
C7 CG331 -0.207 ;C for methyl group CH3
C8 CG331 -0.207 ;C for methyl group CH3
H1 HGA3 0.090 ;alphatic proton, CH3
H2 HGA3 0.090 ;alphatic proton, CH3
H3 HGA3 0.090 ;alphatic proton, CH3
H4 HGA3 0.090 ;alphatic proton, CH3
H5 HGA3 0.090 ;alphatic proton, CH3
H6 HGA3 0.090 ;alphatic proton, CH3
H7 HGA2 0.090 ;alphatic proton, CH2
H8 HGA2 0.090 ;alphatic proton, CH2
H9 HGPAM2 0.330 ;polar H, NEUTRAL methylamine
H10 HGA2 0.090 ;alphatic proton, CH2
H11 HGA2 0.090 ;alphatic proton, CH2
H12 HGPAM2 0.330 ;polar H, NEUTRAL methylamine
H13 HGA2 0.090 ;alphatic proton, CH2
H14 HGA2 0.090 ;alphatic proton, CH2
H15 HGPAM2 0.396 ;polar H, NEUTRAL methylamine
H16 HGPAM2 0.396 ;polar H, NEUTRAL methylamine
H17 HGA1 0.090 ;alphatic proton, CH
H18 HGR52 0.091 ; Aldehyde H, formamide H (RCOH
pdb
ATOM 781 N1 AMA A 130 8.714 54.987 2.676 1.00 47.63 N
ATOM 782 C1 AMA A 130 9.061 56.391 2.868 1.00 47.63 C
ATOM 783 C2 AMA A 130 9.052 57.092 1.516 1.00 47.63 C
ATOM 784 O1 AMA A 130 8.614 58.234 1.401 1.00 47.63 O
ATOM 785 C3 AMA A 130 10.437 56.528 3.519 1.00 76.92 C
ATOM 786 C4 AMA A 130 10.508 55.943 4.915 1.00 76.92 C
ATOM 787 C5 AMA A 130 11.825 56.267 5.593 1.00 76.92 C
ATOM 788 N2 AMA A 130 11.900 55.657 6.916 1.00 76.92 N
ATOM 789 C6 AMA A 130 12.901 55.838 7.770 1.00 76.92 C
ATOM 790 N3 AMA A 130 13.923 56.618 7.443 1.00 76.92 N1+
ATOM 791 N4 AMA A 130 12.882 55.239 8.953 1.00 76.92 N
ATOM 792 C7 AMA A 130 13.991 55.440 9.897 0.00 0.00 C
ATOM 793 C8 AMA A 130 11.752 54.374 9.321 0.00 0.00 C
ATOM 794 H1 AMA A 130 14.312 54.511 10.265 0.00 0.00 H
ATOM 795 H2 AMA A 130 11.340 54.701 10.229 0.00 0.00 H
ATOM 796 H3 AMA A 130 13.667 56.040 10.695 0.00 0.00 H
ATOM 797 H4 AMA A 130 12.088 53.384 9.424 0.00 0.00 H
ATOM 798 H4 AMA A 130 14.787 55.915 9.404 0.00 0.00 H
ATOM 799 H7 AMA A 130 11.020 54.417 8.569 0.00 0.00 H
Fatal error:
Residue 100 named AMA of a molecule in the input file was mapped
to an entry in the topology database, but the atom C used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.